PMFastR: A New Approach to Multiple RNA Structure Alignment

Multiple RNA structure alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Many existing tools for multiple RNA alignments first generate pairwise RNA structure alignments and then build the multiple alignment using only the sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a multiple RNA structure alignment. PMFastR has low memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA. The algorithm also provides a method to utilize a multi-core environment. Finally, we present results on benchmark data sets from BRAliBase, which shows PMFastR outperforms other state-ofthe-art programs. Furthermore, we regenerate 607 Rfam seed alignments and show that our automated process creates similar multiple alignments to the manually-curated Rfam seed alignments.